Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors

TY - JOUR

T1 - Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors

AU - FitzGerald, Edward A.

AU - Vagrys, Darius

AU - Opassi, Giulia

AU - Klein, Hanna F.

AU - Hamilton, David J.

AU - Talibov, Vladimir O.

AU - Abramsson, Mia

AU - Moberg, Anna

AU - Lindgren, Maria T.

AU - Holmgren, Claes

AU - Davis, Ben

AU - O'Brien, Peter

AU - Wijtmans, Maikel

AU - Hubbard, Roderick E.

AU - de Esch, Iwan J.P.

AU - Danielson, U. Helena

N1 - Funding Information: The authors wish to acknowledge support from Eldar Abdurakhmanov and Annette Roos, SciLifeLab Drug Discovery and Development Platform, and library access from the Chemical Biology Consortium Sweden (CBCS). To members of the Danielson Lab for helpful discussions, to Olof Karlsson and the entire team at Cytiva for their continued support with this project. Furthermore, we wish to acknowledge colleagues from Beactica Therapeutics, Matthis Geitmann and Johan Winquist for insightful discussions on fragment screening. The authors also wish to acknowledge Prof. Chris Ulens, Laboratory of Structural Neurobiology, KU Leuven for AChBP expression plasmids and Prof. Yang Shi and Benoit Laurent, Harvard Medical School, for LSD1/CoREST plasmids. Funding Information: This project has received funding from the European Union's Framework Programme for Research and Innovation Horizon 2020 (2014–2020) under the Marie Sklodowska-Curie grant agreement ID 675899 for Fragment based drug discovery Network (FRAGNET) and ID 675555 for Accelerated eEarly stage drug discovery (AEGIS). Funding Information: The authors wish to acknowledge support from Eldar Abdurakhmanov and Annette Roos, SciLifeLab Drug Discovery and Development Platform, and library access from the Chemical Biology Consortium Sweden (CBCS). To members of the Danielson Lab for helpful discussions, to Olof Karlsson and the entire team at Cytiva for their continued support with this project. Furthermore, we wish to acknowledge colleagues from Beactica Therapeutics, Matthis Geitmann and Johan Winquist for insightful discussions on fragment screening. The authors also wish to acknowledge Prof. Chris Ulens, Laboratory of Structural Neurobiology, KU Leuven for AChBP expression plasmids and Prof. Yang Shi and Benoit Laurent, Harvard Medical School, for LSD1/CoREST plasmids. Publisher Copyright: © 2023

PY - 2023/9/14

Y1 - 2023/9/14

N2 - Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.

AB - Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.

KW - Biophysics

KW - Biosensors

KW - Fragment-based drug discovery

KW - SPR

UR - http://www.scopus.com/inward/record.url?scp=85172020784&partnerID=8YFLogxK

U2 - 10.1016/j.slasd.2023.09.001

DO - 10.1016/j.slasd.2023.09.001

M3 - Article

C2 - 37714432

AN - SCOPUS:85172020784

SN - 2472-5552

JO - SLAS Discovery

JF - SLAS Discovery

ER -